Waterproof: educational software for learning how to write mathematical proofs

In order to help students learn how to write mathematical proofs, we developed the educational software called Waterproof (https://github.com/impermeable/waterproof). Waterproof is based on the Coq proof assistant. As students type out their proofs in the program, it checks the logical soundness of each proof step and provides additional guiding feedback. Contrary to Coq proofs, proofs written in Waterproof are similar in style to handwritten ones: proof steps are denoted using controlled natural language, the structure of proofs is made explicit by enforced signposting, and chains of inequalities can be used to prove larger estimates. To achieve this, we developed the Coq library coq-waterproof. The library extends Coq's default tactics using the Ltac2 tactic language. We include many code snippets in this article to increase the number of available Ltac2 examples. Waterproof has been used to supplement teaching the course Analysis 1 at the TU/e for a couple of years. Students started using Waterproof's controlled formulations of proof steps in their handwritten proofs as well; the explicit phrasing of these sentences helps to clarify the logical structure of their arguments.Comment: The Waterproof software can be found at https://github.com/impermeable/waterproof . This article pertains to Waterproof version 0.6.1. The Coq library coq-waterproof can be found at https://github.com/impermeable/coq-waterproof . This article pertains to coq-waterproof version 1.2.

Physiological profile and activity pattern of minor Gaelic football players

The purpose of this study was to evaluate the physiological profile and activity pattern in club- and county-level under-18 (U-18) Gaelic football players relative to playing position. Participants (n = 85) were analyzed during 17 official 15-a-side matches using global positioning system technology (SPI Pro X II; GPSports Systems, Canberra, Australia) and heart rate (HR) telemetry. During the second part of this study, 63 participants underwent an incremental treadmill test to assess their maximal oxygen uptake (V_ o2max) and peak HR (HRmax). Players covered a mean distance of 5,774 6 737 m during a full 60-minute match. The mean %HRmax and %V_ O2max observed during the match play were 81.6 6 4.3% and 70.1 6 7.75%, respectively. The playing level had no effect on the distance covered, player movement patterns, or %HRmax observed during match play. Midfield players covered significantly greater distance than defenders (p = 0.033). Playing position had no effect on %HRmax or the frequency of sprinting or high-intensity running during match play. The frequency of jogging, cruise running, striding (p = 0.000), and walking (p = 0.003) was greater in the midfield position than in the forward position. Time had a significant effect (F(1,39) = 33.512, p-value = 0.000, and h2 Ρ = 0.462) on distance covered and %HRmax, both of which showed a reduction between playing periods. Gaelic football is predominantly characterized by low-to-moderate intensity activity interspersed with periods of high-intensity running. The information provided may be used as a framework for coaches in the design and prescription of training strategies. Positional specific training may be warranted given the comparatively greater demands observed in the midfield playing position. Replicating the demands of match play in training may reduce the decline in distance covered and % HRmax observed during the second half of match play

Interannual variability of primary production and dissolved organic nitrogen storage in the North Pacific Subtropical Gyre

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 117 (2012): G03019, doi:10.1029/2011JG001830.The upper ocean primary production measurements from the Hawaii Ocean Time series (HOT) at Station ALOHA in the North Pacific Subtropical Gyre showed substantial variability over the last two decades. The annual average primary production varied within a limited range over 1991–1998, significantly increased in 1999–2000 and then gradually decreased afterwards. This variability was investigated using a one-dimensional ecosystem model. The long-term HOT observations were used to constrain the model by prescribing physical forcings and lower boundary conditions and optimizing the model parameters against data using data assimilation. The model reproduced the general interannual pattern in the observed primary production, and mesoscale variability in vertical velocity was identified as a major contributing factor to the interannual variability in the simulation. Several strong upwelling events occurred in 1999, which brought up nitrate at rates several times higher than other years and elevated the model primary production. Our model results suggested a hypothesis for the observed interannual variability pattern of primary production at Station ALOHA: Part of the upwelled nitrate input in 1999 was converted to and accumulated as semilabile dissolved organic nitrogen (DON), and subsequent recycling of this semilabile DON supported enhanced primary productivity for the next several years as the semilabile DON perturbation was gradually removed via export.This work was supported in part by the Center for Microbial Oceanography, Research and Education (C-MORE) (NSF EF-0424599), Hawaii Ocean Time series program (NSF OCE09–26766), the Gordon and Betty Moore Foundation, and the Marine Biological Laboratory.2013-03-1

Polyclonality of Concurrent Natural Populations of Alteromonas macleodii

We have analyzed a natural population of the marine bacterium, Alteromonas macleodii, from a single sample of seawater to evaluate the genomic diversity present. We performed full genome sequencing of four isolates and 161 metagenomic fosmid clones, all of which were assigned to A. macleodii by sequence similarity. Out of the four strain genomes, A. macleodii deep ecotype (AltDE1) represented a different genome, whereas AltDE2 and AltDE3 were identical to the previously described AltDE. Although the core genome (∼80%) had an average nucleotide identity of 98.51%, both AltDE and AltDE1 contained flexible genomic islands (fGIs), that is, genomic islands present in both genomes in the same genomic context but having different gene content. Some of the fGIs encode cell surface receptors known to be phage recognition targets, such as the O-chain of the lipopolysaccharide, whereas others have genes involved in physiological traits (e.g., nutrient transport, degradation, and metal resistance) denoting microniche specialization. The presence in metagenomic fosmids of genomic fragments differing from the sequenced strain genomes, together with the presence of new fGIs, indicates that there are at least two more A. macleodii clones present. The availability of three or more sequences overlapping the same genomic region also allowed us to estimate the frequency and distribution of recombination events among these different clones, indicating that these clustered near the genomic islands. The results indicate that this natural A. macleodii population has multiple clones with a potential for different phage susceptibility and exploitation of resources, within a seemingly unstructured habitat

Analysis of drifting SOFAR buoys in the Greenland Sea, 1989-1990

In an attempt to gain a better understanding of the intermediate depth circulation of the Greenland Sea,16 SOFAR floats were launched into Fram Strait in 1988 and 1989. Between the fall of 1989 and the summer of 1990, five of these floats were tracked by autonomous listening stations (ALS) positioned to provide tracking in the southern portion of the Greenland Sea. One float (MZ86) provided tracking information for ten months of the ALS deployment period. The other floats provided tracking information ranging from several days to two months. These float tracks delineated the intermediate depth circulation around the Greenland Sea gyre. The MZ86 trajectory exited the Boreas Basin and crossed the Greenland Fracture Zone with a speed of approximately 17 cm s-1. Along the Greenland continental slope the flow increased to 28 cm s- 1 suggesting the presence of a bottom trapped boundary current. Near 74°N the trajectory turned eastward under the shallower warm core of the Jan Mayen Current at 4 cm s-1. This leg closed the Greenland Sea gyre and also shows evidence of interactions with filaments of the Norwegian Atlantic Current (NAC) coming through the Mohns Ridge at these intermediate depths. Two other floats demonstrated tracks which crossed the Mohns Ridge and drifted farther to the east, mixing with the waters of the NAC.http://archive.org/details/analysisofdrifti00mccaLieutenant Commander, United States NavyApproved for public release; distribution is unlimited

Comparison of sprint interval and endurance training in team sport athletes

High volume endurance training (ET) has traditionally been used to improve aerobic capacity but is extremely time-consuming in contrast to low-volume short-duration sprint interval training (SIT) that improves maximal oxygen uptake (V_ O2max) to a similar extent. Few studies have compared the effects of SIT vs. ET using running-based protocols, or in team sport athletes. Club level male Gaelic football players were randomly assigned to SIT (n = 7; 21.6 6 2.1 years) or ET (n = 8; 21.9 6 3.5 years) for 6 sessions over 2 weeks. V_ O2max, muscle mitochondrial enzyme activity, running economy (RE), and high-intensity endurance capacity (HEC) were measured before and after training. An increase in V_ O2max (p # 0.05) after 2 weeks of both SIT and ET was observed. Performance in HEC increased by 31.0 and 17.2% after SIT and ET, respectively (p # 0.05). Running economy assessed at 8, 9, 10, and 11 km$h 21 , lactate threshold and vV_ O2max were unchanged after both SIT and ET. Maximal activity of 3-b-hydroxylacyl coenzyme A dehydrogenase (b-HAD) was increased in response to both SIT and ET (p #0.05), whereas the maximal activity of citrate synthase remained unchanged after training (p = 0.07). A running-based protocol of SIT is a time-efficient training method for improving aerobic capacity and HEC, and maintaining indices of RE and lactate threshold in team sport athletes

Decomposition of monolith applications Into microservices architectures: a systematic review

Microservices architecture has gained significant traction, in part owing to its potential to deliver scalable, robust, agile, and failure-resilient software products. Consequently, many companies that use large and complex software systems are actively looking for automated solutions to decompose their monolith applications into microservices. This paper rigorously examines 35 research papers selected from well-known databases using a Systematic Literature Review (SLR) protocol and snowballing method, extracting data to answer the research questions, and presents the following four contributions. First, the Monolith to Microservices Decomposition Framework (M2MDF) which identifies the major phases and key elements of decomposition. Second, a detailed analysis of existing decomposition approaches, tools and methods. Third, we identify the metrics and datasets used to evaluate and validate monolith to microservice decomposition processes. Fourth, we propose areas for future research. Overall, the findings suggest that monolith decomposition into microservices remains at an early stage and there is an absence of methods for combining static, dynamic, and evolutionary data. Insufficient tool support is also in evidence. Furthermore, standardised metrics, datasets, and baselines have yet to be established. These findings can assist practitioners seeking to understand the various dimensions of monolith decomposition and the community's current capabilities in that endeavour. The findings are also of value to researchers looking to identify areas to further extend research in the monolith decomposition space

Position paper on high performance computing needs in earth system prediction

The article of record as published may be found at http://dx.doi.org/10.7289/V5862DH3The United States experiences some of the most severe weather on Earth. Extreme weather or climate events - such as hurricanes, tornadoes, flooding, drought, and heat waves - can devastate communities and businesses, cause loss of life and property, and impact valuable infrastructure and natural resources. The number and severity of extreme weather and climate events in the U.S. has risen since 1980, and is projected to continue rising this century. Growing populations in vulnerable areas create increased risks. If current trends continue, damages from extreme weather and climate events could grow four-fold by 2050. Predictions and projections of weather and extreme events across time scales from weather to climate rely on sophisticated numerical models running on High Performance Computing (HPC) systems, which press the frontier of the Nation’s HPC capability. The Nation’s Earth system modeling community has a unique set of HPC requirements which differ from industry needs. Typically, HPC advances are measured using computational peak performance metrics that are ill-suited to Earth system modeling applications. We advocate for a shift in processor design to increase emphasis on memory bandwidth, so Earth system models run more efficiently and better serve the public need

Computational methods for early predictive safety assessment from biological and chemical data

Introduction The goal of early predictive safety assessment (PSA) is to keep compounds with detectable liabilities from progressing further in the pipeline. Such compounds jeopardize the core of pharmaceutical research and development and limit the timely delivery of innovative therapeutics to the patient. Computational methods are increasingly used to help understand observed data, generate new testable hypotheses of relevance to safety pharmacology, and supplement and replace costly and time-consuming experimental procedures. Areas covered We survey methods operating on different scales of both physical extension and complexity. After discussing methods used to predict liabilities associated with structures of individual compounds we review the use of adverse event data and safety profiling panels. We finish with examining the complexities of toxicology data from animal experiments, and how these data can be mined. Expert opinion We discuss factors that will significantly advance the field of PSA such as data warehousing, sharing of data, and the use of standard ontologies for data relevant to safety assessment. We provide an outlook of how compound liabilities can be addressed by front-loading screening campaigns with focused sets of compounds. Additionally, we discuss how improved hit assessment of such campaigns can benefit the early termination of undesirable compounds

Comparative Microbiome Diversity Analysis of Mexican Aquaculture Facilities and Coastal Habitats

<p>Microorganisms play a critical role in global ecological balance. In pristine areas the measurement of the microbial diversity in aquatic samples can serve to establish the baseline for future local management of these areas, and provides a basis of comparison to other sites. We have collected water samples from a range of locations along the coasts of the Caribbean Sea and Pacific Ocean in Baja California Sur, Quintana Roo, and Sinaloa. The sites sampled included mangrove lagoons, tide pools, coastal lagoons and estuaries, as well as aquaculture facilities.</p> <p>Total DNA was extracted from eleven of the collected water samples and then shotgun sequenced using three Illumina HiSeq 2000 lanes. The corresponding sequences were classified using QuickTaxa™, our novel bioinformatics pipeline. In short, QuickTaxa™ efficiently identifies and extracts 16S/18S rRNA sequence reads from shotgun metagenomic datasets, and then classifies them using a version of the RDP Classifier, which had been trained using a custom training set consisting of both 16S and 18S rRNA sequences. The results were then formatted for display and analysis using Krona interactive plots. The QuickTaxa™ analysis showed that most samples exhibited a relatively large and evenly distributed number of species, which may indicate a balanced ecosystem with many different ecological niches.</p> <p>In contrast, one sample, which was collected in the effluent waters of a thermoelectric plant, exhibited a relatively low diversity of species, which may reflect environmental perturbation and selection for few opportunistic microorganisms. In addition to the QuickTaxa™ analysis, the complete metagenomic datasets were individually assembled into contigs with a combined assembly size of 2.8 Gbp, of which a selected subset was functionally annotated using SGI’s Archetype® bioinformatics analysis platform. In contrast to assembly and functional annotation of shotgun metagenomic datasets, which are typically very computationally intensive, the QuickTaxa™ pipeline enables almost instantaneous analysis of the microbiome diversity of large metagenomic datasets.</p